PFRMAT SS 
TARGET T0084 
AUTHOR 9271-4485-8460 
REMARK 
METHOD  Automated I-SITES + ROSETTA 
METHOD  ========================================================= 
METHOD  Predictions from this group are of local and 
METHOD  supersecondary structure. They should be evaluated 
METHOD  on an approximate length scale of 20-30 residues. Although 
METHOD  Some effort has been made to pack the local structure 
METHOD  predictions into a globular form, the effectiveness 
METHOD  of this procedure is untested.   
METHOD 
METHOD  The method was NOT OPTIMIZED FOR SECONDARY STRUCTURE 
METHOD  prediction. This predictions is only meant to supplement the  
METHOD  corresponding TS prediction. 
METHOD  ========================================================= 
METHOD 
METHOD (1) Psi-blast was used to obtain an alignment 
METHOD (2) The PHD prediction server was used to obtain a 3-state  
METHOD     prediction (optional) 
METHOD (3) The I-sites method (JMB 281(3):565-577) 
METHOD     was used to predict backbone angles and  
METHOD     confidences. Secondary structure assignments were 
METHOD     made according to the secondary structure (DSSP) 
METHOD     assignments of the fragments used to build the local 
METHOD     structure. 
METHOD  
METHOD >>>>THIS METHOD IS TOTALLY AUTOMATED!! <<<< 
METHOD In constrast to earlier CASP3 
METHOD methods from this (D. Baker) lab. The submissions from this 
METHOD group ("C.Bystroff") are made automatically with no manual 
METHOD intervention. The method will be available via WWW server, 
METHOD after CASP3. The URL is http://ganesh.bchem.washington.edu/ 
METHOD ~bystroff/Isites/ISLserver2.html 
METHOD     >>> no PHD predictions were used (model 2) 
MODEL 2  
C C 0.00 
G C 0.00 
G H 0.17 
R H 0.38 
E H 0.54 
G H 0.68 
V H 0.68 
L H 0.68 
K H 0.71 
K H 0.73 
L H 0.73 
R C 0.83 
A C 0.92 
V H 0.84 
E H 0.75 
N H 0.75 
E H 0.74 
L H 0.73 
H H 0.68 
Y C 0.69 
N H 0.76 
K H 0.81 
S H 0.85 
L H 0.85 
L H 0.85 
E H 0.87 
E H 0.89 
V H 0.91 
K H 0.94 
D H 0.94 
E H 0.94 
L H 0.94 
Q H 0.91 
K H 0.89 
M H 0.89 
R H 0.81 
Q C 0.36 
END 
